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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation. | TianGzlab/ | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 2 | Load when discovering bulk gene co-expression modules and hub genes with R WGCNA. | TianGzlab/ | 161 | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 3 | A skill your agent uses when a tabular dataset (CSV, Excel, Parquet, Stata, SAS) needs a data dictionary. | Aperivue/ | 331 | — | ~1.1k | Automated safety check: Pass | MIT | 4 days ago |
| 4 | 4.Arboreto Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. | K-Dense-AI/ | 48k | 1 repo | ~2.7k | Automated safety check: Pass | BSD-3-Clause | 4 days ago |
| 5 | Fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames… | ClawBio/ | 1.2k | — | ~3.4k | Automated safety check: Pass | Apache-2.0 | yesterday |
| 6 | Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data. | K-Dense-AI/ | 48k | 1 repo | ~3.2k | Automated safety check: Notes | Apache-2.0 | 4 days ago |
| 7 | Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq. | TianGzlab/ | 161 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 8 | Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and… | GPTomics/ | 1.2k | 1 repo | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 9 | Loads mass-spectrometry data into Python/R and strips the search engine's bookkeeping before any number is trusted -- removes decoys (REV/Reverse), contaminants (CON/Potential contaminant)… | GPTomics/ | 1.2k | 1 repo | ~4.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 10 | Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relative intensities, normalized RT, optional CCS), covering experimental DDA… | GPTomics/ | 1.2k | 1 repo | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 11 | Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 371 | 2 repos | ~4k | Automated safety check: Pass | Apache-2.0 | 10 days ago |
| 12 | Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit… | GPTomics/ | 1.2k | 1 repo | ~5.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 13 | Analyzes data-independent acquisition (DIA) proteomics by scoring reconstructed fragment-chromatogram peak groups against a decoy null with DIA-NN (library-free directDIA, library-based, or… | GPTomics/ | 1.2k | 1 repo | ~5.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 14 | Julia-based econometric and structural estimation for computationally intensive tasks. | brycewang-stanford/ | 4.5k | — | ~1.4k | Automated safety check: Pass | Unknown | 4 days ago |
| 15 | 15.Review R R code review for the sewage project. An agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. | brycewang-stanford/ | 4.5k | — | ~1.3k | Automated safety check: Pass | Unknown | 4 days ago |
| 16 | GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). | jaechang-hits/ | 371 | 2 repos | ~5.3k | Automated safety check: Pass | BSD-3-Clause | 10 days ago |
| 17 | Compute aerospace environment properties including atmosphere (ISA, COESA, NRLMSISE-00, non-standard, CIRA), gravity (spherical harmonic, WGS84, zonal, centrifugal), horizontal wind (HWM), magnetic… | matlab/ | 1.1k | — | ~4.2k | Automated safety check: Pass | Unknown | yesterday |
| 18 | Load when placing bulk RNA-seq samples on a single-cell reference's pseudotime axis (NNLS deconvolution + nearest-neighbour mapping). | TianGzlab/ | 161 | — | ~1.6k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 19 | Load when ingesting a MaxQuant proteinGroups.txt, FragPipe combinedprotein.tsv, DIA-NN report, or generic CSV / TSV protein-quantification table — normalises columns to a standard schema, emits… | TianGzlab/ | 161 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 20 | Load when summarising cross-linking MS (XL-MS) results — intra/inter-protein link split, optional FDR filtering, distance-constraint validation against a per-crosslinker (DSS / BS3 / EDC / DSSO /… | TianGzlab/ | 161 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 21 | Load when testing whether cell-type / cluster proportions or neighbourhood densities differ between conditions in a multi-sample scRNA AnnData via Milo, scCODA, simple proportion screen, or R… | TianGzlab/ | 161 | — | ~2.1k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 22 | 22.Sc Grn Load when inferring TF → target gene regulatory networks on a normalised scRNA AnnData via pySCENIC (GRNBoost2 + cisTarget + AUCell) or correlation-based GRN fallback (when arboreto is unavailable… | TianGzlab/ | 161 | — | ~1.7k | Automated safety check: Pass | Apache-2.0 | 2 days ago |
| 23 | Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology… | jaechang-hits/ | 371 | 1 repo | ~5.5k | Automated safety check: Pass | BSD-3-Clause | 10 days ago |
| 24 | A skill your agent uses for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration… | VectorSpaceLab/ | 330 | — | ~946 | Automated safety check: Pass | BSD-3-Clause | 1 mo ago |
| 25 | Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. | bioMate-AI/ | 804 | — | ~968 | Automated safety check: Pass | Unknown | 3 mo ago |
